improved error reporting

nextgenusfs · Mar 31, 2016 · 552c67c · 552c67c
1 parent 081509e
commit 552c67c
Showing 1 changed file with 7 additions and 1 deletion.
diff --git a/bin/funannotate-predict.py b/bin/funannotate-predict.py
@@ -71,6 +71,12 @@ def __init__(self,prog):
 version = lib.get_version()
 lib.log.info("Running %s" % version)
 
+#check for DB files needed for funanntoate predict, should only need REPEAT DB
+blastdb = os.path.join(parentdir,'DB','REPEATS.psq')
+if not os.path.isfile(blastdb):
+    lib.log.error("funannotate database is not properly configured, please run `./setup.sh` in the %s directory" % parentdir)
+    os._exit(1)
+
 #do some checks and balances
 try:
     EVM = os.environ["EVM_HOME"]
@@ -134,7 +140,7 @@ def __init__(self,prog):
     args.protein_evidence = os.path.join(parentdir, 'DB', 'uniprot_sprot.fasta')
 
 #check input files to make sure they are not empty
-input_checks = [args.genemark_mod, args.protein_evidence, args.transcript_evidence, args.exonerate_proteins, args.gmap_gff, args.pasa_gff, args.repeatmodeler_lib, args.rna_bam]
+input_checks = [args.input, args.genemark_mod, args.protein_evidence, args.transcript_evidence, args.exonerate_proteins, args.gmap_gff, args.pasa_gff, args.repeatmodeler_lib, args.rna_bam]
 for i in input_checks:
     if i:
         lib.checkinputs(i)